Once you're on the ship, enter through the door on your left. Go down the stairs on your right. On the next floor, go right, into the small corridor and enter the door on the left wall. Sprint across the sand and go down the stairs at the end of the path. Make your way through this corridor until Fi prompts you about the sealed door. Continue forward into the next room. The combination for the lock is down-up-down-right. Enter the room and get the small key. Backtrack all the way to the top and enter the locked door next to the bird statue.
Go back to the deck and hit the switch Fi showed you earlier with an arrow. Go around the mast and climb up the ladder. Use the bow to shoot the far-away switches, allowing you to zipline across. Do this until you reach the top, thrust your sword into the lock the Bokoblin locked earlier, and unlock it.Jump back down and enter the same door as before. Make your way down to the quicksand, and enter the door on the left, the one with the sunrays. Shoot an arrow through the grate on the ceiling to hit the timeshift stone. Pick up the map from the chest, pull the lever and exit. Sprint across the quicksand and shoot an arrow onto the switch through the small ventilation opening on the right wall. Enter the room to the left of the opening. There's a block to your right blocking another small opening, push it away. Stand on the switch and shoot an arrow through the opening. Head back across the quicksand and re-activate the timeshift stone. Enter the first door on the right once you're in the corridor, and thrust your sword into the machine. Activate it, and exit. Now enter the second door on the left wall. Push the block onto the switch as per usual. Go all the way back now, outside of the boat, and go to the rescue boat on the opposite end. Hit the target on the crane that holds the rescue boat to make it descend. Now hit the timeshift stone to deactivate it and drop down onto the boat. Enter the room from here, and go to the section with the generator. Hit the timeshift stone from the opening in the ceiling to reactivate it and turn on the generator. Enter the room with the two windows again and drop down the left window, down the ladder. Enter the engine room and jump down.
Go back into the main section of the ship, down to the control room door. Rotate the carving into place and enter the boss room.